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Independent Section

Contains tests that are independent of the class of modeled organism, a model's complexity or types of identifiers that are used to describe its components. Parameterization or initialization of the network is not required. See readme for more details.

Consistency

Stoichiometric Consistency

100.0%

Mass Balance

100.0%

Charge Balance

94.7%

Metabolite Connectivity

100.0%

Unbounded Flux In Default Medium

78.5%

A large fraction of model reactions able to carry unlimited flux under default conditions indicates problems with reaction directionality, missing cofactors, incorrectly defined transport reactions and more. Implementation: Without changing the default constraints run flux variability analysis. From the FVA results identify those reactions that carry flux equal to the model's maximal or minimal flux.

A fraction of 21.53% of the non-blocked reactions (in total 90 reactions) can carry unbounded flux in the default model condition. Unbounded reactions may be involved in thermodynamically infeasible cycles: rxn00973_c, rxn01358_c, rxn01547_c, rxn00910_c, rxn01102_c, ...

["rxn00973_c","rxn01358_c","rxn01547_c","rxn00910_c","rxn01102_c","rxn08976_c","rxn03185_c","rxn00926_c","rxn00171_c","rxn00612_c","rxn02159_c","rxn02380_c","rxn08799_c","rxn01280_c","rxn01301_c","rxn00499_c","rxn00146_c","rxn00182_c","rxn08815_c","rxn01281_c","rxn03642_c","rxn10114_c","rxn01211_c","rxn08850_c","rxn00500_c","rxn00606_c","rxn02811_c","rxn03062_c","rxn00863_c","rxn00908_c","rxn01138_c","rxn08820_c","rxn00145_c","rxn00297_c","rxn03481_c","rxn00611_c","rxn01106_c","rxn08647_c","rxn03366_c","rxn08025_c","rxn12191_c","rxn02789_c","rxn01977_c","rxn01302_c","rxn00459_c","rxn01208_c","rxn03467_c","rxn08818_c","rxn08655_c","rxn04954_c","rxn03365_c","rxn05226_c","rxn03641_c","rxn02171_c","rxn00355_c","rxn00558_c","rxn01388_c","rxn01649_c","rxn00085_c","rxn00974_c","rxn06760_c","rxn03004_c","rxn10770_c","rxn08797_c","rxn06759_c","rxn08657_c","rxn00157_c","rxn01236_c","rxn05289_c","rxn00493_c","EX_cpd00001_e","EX_cpd00027_e","rxn30075_c","rxn21134_c","rxn13022_c","rxn02167_c","rxn13713_c","rxn00871_c","EX_cpd00029_e","rxn08061_c","rxn08686_c","rxn09142_c","rxn09145_c","rxn09341_c","rxn09147_c","rxn00605_c","rxn09126_c","rxn09124_c","rxn09348_c","rxn09163_c"]

Sub Total

96%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{94.74 + 78.47 + (3 \cdot 100) +}{(5 \cdot 100)} = 96.17$ $(94.74 + 78.47 + (3 * 100) + )/((5 * 100)) = 96.17$

Annotation - Metabolites

Presence of Metabolite Annotation

100.0%

Metabolite Annotations Per Database

pubchem.compound

0.0%

kegg.compound

0.4%

seed.compound

99.5%

inchikey

0.0%

inchi

0.0%

chebi

0.0%

hmdb

0.0%

reactome

0.0%

metanetx.chemical

0.0%

bigg.metabolite

0.0%

biocyc

0.0%

Metabolite Annotation Conformity Per Database

pubchem.compound

0.0%

kegg.compound

100.0%

A total of 0 metabolite annotations (0.00%) do not match the regular expression patterns defined on identifiers.org for the kegg.compound database:

seed.compound

100.0%

inchikey

0.0%

inchi

0.0%

chebi

0.0%

hmdb

0.0%

reactome

0.0%

metanetx.chemical

0.0%

bigg.metabolite

0.0%

biocyc

0.0%

Uniform Metabolite Identifier Namespace

100.0%

Sub Total

57%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{0.35 + 99.47 + (4 \cdot 100) + (18 \cdot 0)}{(24 \cdot 100)} = 56.81$ $(0.35 + 99.47 + (4 * 100) + (18 * 0))/((24 * 100)) = 56.81$

Annotation - Reactions

Presence of Reaction Annotation

100.0%

Reaction Annotations Per Database

rhea

0.0%

kegg.reaction

1.0%

seed.reaction

97.9%

The following 24 reactions (2.11%) lack annotation for seed.reaction: R03018_c, COG3601_c, ID010_c, ENOG4108HXH_c, R01174_1_c, ...

metanetx.reaction

0.0%

bigg.reaction

0.0%

reactome

0.0%

ec-code

0.0%

brenda

0.0%

biocyc

0.0%

Reaction Annotation Conformity Per Database

rhea

0.0%

kegg.reaction

99.9%

seed.reaction

90.6%

metanetx.reaction

0.0%

bigg.reaction

0.0%

reactome

0.0%

ec-code

0.0%

brenda

0.0%

biocyc

0.0%

Uniform Reaction Identifier Namespace

100.0%

Sub Total

58%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{0.97 + 97.89 + 99.91 + 90.57 + (2 \cdot 100) + (14 \cdot 0)}{(20 \cdot 100)} = 58.04$ $(0.97 + 97.89 + 99.91 + 90.57 + (2 * 100) + (14 * 0))/((20 * 100)) = 58.04$

Annotation - Genes

Presence of Gene Annotation

100.0%

Gene Annotations Per Database

refseq

100.0%

uniprot

0.0%

ecogene

0.0%

kegg.genes

0.0%

ncbigi

0.0%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Gene Annotation Conformity Per Database

refseq

100.0%

uniprot

0.0%

ecogene

0.0%

kegg.genes

0.0%

ncbigi

0.0%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Sub Total

40%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(3 \cdot 100) + (18 \cdot 0)}{(21 \cdot 100)} = 40.00$ $((3 * 100) + (18 * 0))/((21 * 100)) = 40.00$

Annotation - SBO Terms

Metabolite General SBO Presence

100.0%

Metabolite SBO:0000247 Presence

100.0%

Reaction General SBO Presence

100.0%

Metabolic Reaction SBO:0000176 Presence

100.0%

Transport Reaction SBO:0000185 Presence

100.0%

Exchange Reaction SBO:0000627 Presence

100.0%

Demand Reaction SBO:0000628 Presence

Skipped

Sink Reactions SBO:0000632 Presence

100.0%

Gene General SBO Presence

100.0%

Gene SBO:0000243 Presence

100.0%

Biomass Reactions SBO:0000629 Presence

100.0%

Sub Total

91%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(10 \cdot 100) + (1 \cdot 0)}{(11 \cdot 100)} = 90.91$ $((10 * 100) + (1 * 0))/((11 * 100)) = 90.91$

Total Score

85%

The Total Score is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(3 \cdot 96.17) + (1 \cdot 56.81) + (1 \cdot 58.04) + (1 \cdot 40.00) + (2 \cdot 90.91)}{(3 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (2 \cdot 100)} = 85.17$ $((3 * 96.17) + (1 * 56.81) + (1 * 58.04) + (1 * 40.00) + (2 * 90.91))/((3 * 100) + (1 * 100) + (1 * 100) + (1 * 100) + (2 * 100)) = 85.17$

Total Score

85%

Score per Category

Specific Section

Covers general statistics and specific aspects of a metabolic network that are not universally applicable. See readme for more details.

SBML

SBML Level and Version

Errored

FBC enabled

Errored

Basic Information

Model Identifier

iCdR758

Total Metabolites

1,140

Total Reactions

1,135

Total Genes

758

Total Compartments

Metabolic Coverage

1.50

Metabolite Information

Unique Metabolites

1,140

Duplicate Metabolites in Identical Compartments

Metabolites without Charge

Metabolites without Formula

Medium Components

Reaction Information

Purely Metabolic Reactions

923

Purely Metabolic Reactions with Constraints

Transport Reactions

104

Transport Reactions with Constraints

Thermodynamic Reversibility of Purely Metabolic Reactions

1.00

Reactions With Partially Identical Annotations

0.00

Duplicate Reactions

0.00

Reactions With Identical Genes

0.54

Gene-Protein-Reaction (GPR) Associations

Reactions without GPR

213

Fraction of Transport Reactions without GPR

0.45

Enzyme Complexes

Errored

Biomass

Biomass Reactions Identified

Biomass Consistency

teichoicacid_rxn

1.49

peptidoglycan_rxn

2.77

biomass

0.02

protein_rxn

0.64

lipid_rxn

0.03

cellwall_rxn

0.00

rna_rxn

0.55

cofactor_rxn

0.09

dna_rxn

1.23

Biomass Production In Default Medium

teichoicacid_rxn

0.25

peptidoglycan_rxn

7.35

biomass

24.51

protein_rxn

9.80

lipid_rxn

1.23

cellwall_rxn

4.90

rna_rxn

3.68

cofactor_rxn

4.90

dna_rxn

1.23

Unrealistic Growth Rate In Default Medium

teichoicacid_rxn

false

peptidoglycan_rxn

true

biomass

true

protein_rxn

true

lipid_rxn

false

cellwall_rxn

true

rna_rxn

true

cofactor_rxn

true

dna_rxn

false

Biomass Production In Complete Medium

teichoicacid_rxn

0.90

peptidoglycan_rxn

26.98

biomass

89.94

protein_rxn

35.98

lipid_rxn

4.50

cellwall_rxn

17.99

rna_rxn

13.49

cofactor_rxn

17.99

dna_rxn

4.50

Blocked Biomass Precursors In Default Medium

teichoicacid_rxn

peptidoglycan_rxn

biomass

protein_rxn

lipid_rxn

cellwall_rxn

rna_rxn

cofactor_rxn

dna_rxn

Blocked Biomass Precursors In Complete Medium

teichoicacid_rxn

peptidoglycan_rxn

biomass

protein_rxn

lipid_rxn

cellwall_rxn

rna_rxn

cofactor_rxn

dna_rxn

Ratio of Direct Metabolites in Biomass Reaction

teichoicacid_rxn

0.00

peptidoglycan_rxn

0.00

biomass

0.00

protein_rxn

0.00

lipid_rxn

0.00

cellwall_rxn

0.00

rna_rxn

0.00

cofactor_rxn

0.29

dna_rxn

0.00

Number of Missing Essential Biomass Precursors

teichoicacid_rxn

peptidoglycan_rxn

biomass

protein_rxn

lipid_rxn

cellwall_rxn

rna_rxn

cofactor_rxn

dna_rxn

Energy Metabolism

Non-Growth Associated Maintenance Reaction

Growth-associated Maintenance in Biomass Reaction

teichoicacid_rxn

false

peptidoglycan_rxn

false

biomass

false

protein_rxn

false

lipid_rxn

false

cellwall_rxn

false

rna_rxn

false

cofactor_rxn

false

dna_rxn

false

Number of Reversible Oxygen-Containing Reactions

Erroneous Energy-generating Cycles

MNXM3

Skipped

MNXM63

Skipped

MNXM51

Skipped

MNXM121

Skipped

MNXM423

Skipped

MNXM6

Skipped

MNXM10

Skipped

MNXM38

Skipped

MNXM208

Skipped

MNXM191

Skipped

MNXM223

Skipped

MNXM7517

Skipped

MNXM12233

Skipped

MNXM558

Skipped

MNXM21

Skipped

MNXM89557

Skipped

Network Topology

Universally Blocked Reactions

482

Orphan Metabolites

Dead-end Metabolites

Stoichiometrically Balanced Cycles

Metabolite Production In Complete Medium

515

Metabolite Consumption In Complete Medium

551

Matrix Conditioning

Ratio Min/Max Non-Zero Coefficients

0.00

Independent Conservation Relations

194

Rank

946

Degrees Of Freedom

189

Experimental Data Comparison

Growth Prediction

Skipped

Gene Essentiality Prediction

Skipped

Misc. Tests

Environment

Python Version 3.6.9

Platform Linux

Memote Version 0.9.12

Package Versions